Critique of "Toppling Another Evolutionary Icon, ENCODE Data Suggests Endogenous Retroviruses Are Functional"

Original article by Casey Luskin of Evolution News and Views, 7th September 2015.

This Critique by Barry Desborough 9th September 2015.

Quotes from Luskin’s article are indented. But we start with the phrase in the title, “Another Evolutionary Icon”. We know immediately that we are in for a propaganda piece. Nowhere in the article is there justification that any other “evolutionary icon” has been toppled. Are we expected to just take Luskin’s word for it? Moving on…

Luskin’s article was produced in response to an email sent by a participant in the discussion of the video, “Genomic Expert Debunks The Evolutionits [sic] ERV Argument - Evolution Debate”.

She commented, “I emailed Discovery Inst and asked them about your claim of the 200,000 shared ERVs (between chimps and humans) and I got a personal email from Casey Luskin and also, this article was the result of my inquiry which you will find interesting, I am sure.”

Luskin’s reply begins:-

Recently a reader emailed us to ask about how to respond to the argument that some endogenous retroviruses (ERVs) seem to match the standard phylogeny of higher primates, supporting common descent.

(Actually, this is not the argument at all. I know that Luskin does know what the actual argument is. I wonder why he ignores it.)

Endogenous retroviruses are thought to be parasitic junk sequences in our genome that were derived from viral DNA. Evolutionists often cite them as supposed evidence of common ancestry. The reader asked how many ERVs are shared between humans and apes. These are good questions. ERVs are a favorite with Darwin defenders --

Nobody is “Defending Darwin”. We are defending all the sciences that are rejected by creationists for politico-religious reasons, including biology, geology, cosmology, physics etc.

so much so that one particularly uncivil activist, Abbie Smith, even named her popular science blog after them, "ERV."

Abbie Smith is an active research scientist. A virologist. She certainly doesn’t suffer fools and liars gladly. Luskin fails to link to her blog so that you can judge for yourselves easily. It is here. But whether or not Abbie is “uncivil” or not is irrelevant. What matters is if she is right.

In response, I suggested that, when analyzing common descent, the number of ERVs shared by humans and chimps is beginning to look like it's not a very important question.

It is a vital question, and it is very telling that Luskin avoids it. It is answered and the answer is explained here. The whole thrust of the ERV evidence for common descent is that the only way in which large numbers of ERVs can have arrived at corresponding locations in the genomes of species that evolutionary science has already deduced are closely related, is this: Common ancestors acquired proviral integrations in their germline DNA, and these have been inherited. The argument is summarized here.

An assumption in the question (and in the arguments from supporters of common ancestry) is that ERVs are a type of functionless "junk" DNA.

This is a deliberate, knowing straw-man. And as such, it is tantamount to a bald-faced lie. See the argument linked to above. Nowhere does it appeal to ERVs being “junk” and being totally without function. It notes that some parts of some ERVs are functional - even vital in some cases. It seems that attacking a straw-man is the only “argument” creationists have to put up. And so it goes.

Thus if apes and humans share ERVs in the same position in our genomes, that would seemingly count as evidence for common descent. But what if ERVs aren't junk? What if they are a type of functional DNA? If that's the case, then shared ERVs could easily be explained by common design rather than common descent, and they would certainly no longer be some kind of special argument for common ancestry.

Here are the problems with this attack on his poor straw-man.
ERVs do stuff. Doesn't that prove that they didn't originate from retroviruses, but were designed?
But how can you rule out design as an explanation?

In fact there is good evidence that ERVs as a class of DNA are functional. A 2013 paper in PLOS Genetics using ENCODE data reported that very high percentages of endogenous retroviruses in the human genome are associated with open chromatin -- strong evidence of transcription -- and that they are transcribed non-randomly, suggesting some functional role:

It is hard to believe that Casey Luskin, active blogger for “Evolution News and Views” has never heard of natural selection! Integrate viral DNA willy-nilly into an existing genome. Those integrations are going to either be detrimental, neutral or advantageous with respect to the chances of the host and the sequence itself getting reproduced. Guess which ones will get flushed from the genome, even if they make it to a second generation? Guess which ones will be positively selected for? Of course the surviving components are going to be transcribed non-randomly! Their role in cancers, by the way, is understandable in terms of natural selection too. Late-onset diseases, as cancers generally are, are not selected against if you die of them well after reproductive age, or if, as in the past, you were more likely to die of something else at a younger age anyway. Is cancer induction a designed-in function? Does Luskin really believe this?

Luskin continues to blather on about his straw-man “junk-DNA defenders” and functionality (functionality that “evolutionists” have discovered). It is interesting to note that no “discovery” or “creation research” “institutes” have conducted this, or any other research.

So Luskin fails to answer the question posed, which was, just how many ERVs and ERV fragments are commonly located in the DNA of chimps and humans? He is well aware of how many, his colleague having attempted to critique this article, the critique having been rebutted here. (Well worth the read as an analysis of “Jonathan M”’s M.O.)

Here are more questions Luskin may wish to avoid.

• Why, if ERVs are designed into our genomes, did the “Phoenix” virus experiment succeed in resurrecting a fully functional exogenous retrovirus?
• Why, if ERVs are not of retroviral origin, do they exhibit a viral codon bias?
• If ERVs are not of retroviral origin, what is the intended design function of reverse transcriptase, integrase and transcribable LTRs?
• What is his explanation for the existence of exogenous and endogenous instances of KoRV?

Creationists have no answers to the case for common descent from commonly-located endogenous retroviruses. The characterization of the argument as being one from similarity is incorrect. The characterization of it as an argument from the existence of “junk” is a nonsense straw-man argument. Creationists often say that they have the same data, but interpret it differently. With ERVs, they fail utterly to produce an interpretation of the information, preferring to ignore it and create smoke-screens.

The reality is that ERVs are derived from retroviruses, and that commonly located retroviruses are commonly located because they are commonly inherited. This puts it beyond any reasonable doubt that Charlie the chimp is Casey Luskin’s, yours and my cousin.